Hey Mark,
For the Bio::DB::Genbank route, I think get_stream_by_query() will take a
list of accessions and automatically make a batch query.
You might also try looking at the EUtilities Cookbook HOWTO to see if that
fits your bill.
Apologies for not being more specific: I rarely need to do this in an
automated fashion myself, so I usually just do boring ol' Batch Entrez
retrieval on the website.
Hope that helps,
Dave